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<a href="particle__dynamics__diffusion__reaction_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/* -----------------------------------------------------------------------------*</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment"> *                               SPHinXsys                                      *</span></div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment"> * -----------------------------------------------------------------------------*</span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment"> * SPHinXsys (pronunciation: s&#39;finksis) is an acronym from Smoothed Particle    *</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment"> * Hydrodynamics for industrial compleX systems. It provides C++ APIs for       *</span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment"> * physical accurate simulation and aims to model coupled industrial dynamic    *</span></div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment"> * systems including fluid, solid, multi-body dynamics and beyond with SPH      *</span></div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment"> * (smoothed particle hydrodynamics), a meshless computational method using     *</span></div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment"> * particle discretization.                                                     *</span></div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;<span class="comment"> *                                                                              *</span></div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="comment"> * SPHinXsys is partially funded by German Research Foundation                  *</span></div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment"> * (Deutsche Forschungsgemeinschaft) DFG HU1527/6-1, HU1527/10-1,               *</span></div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment"> * HU1527/12-1 and HU1527/12-4.                                                 *</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment"> *                                                                              *</span></div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment"> * Portions copyright (c) 2017-2022 Technical University of Munich and          *</span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment"> * the authors&#39; affiliations.                                                   *</span></div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment"> *                                                                              *</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment"> * Licensed under the Apache License, Version 2.0 (the &quot;License&quot;); you may      *</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment"> * not use this file except in compliance with the License. You may obtain a    *</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment"> * copy of the License at http://www.apache.org/licenses/LICENSE-2.0.           *</span></div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment"> *                                                                              *</span></div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment"> * -----------------------------------------------------------------------------*/</span></div><div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="preprocessor">#ifndef PARTICLE_DYNAMICS_DIFFUSION_REACTION_H</span></div><div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="preprocessor">#define PARTICLE_DYNAMICS_DIFFUSION_REACTION_H</span></div><div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;</div><div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="preprocessor">#include &quot;all_particle_dynamics.h&quot;</span></div><div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="preprocessor">#include &quot;<a class="code" href="diffusion__reaction__particles_8h.html">diffusion_reaction_particles.h</a>&quot;</span></div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#include &quot;diffusion_reaction.h&quot;</span></div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;</div><div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="keyword">namespace </span><a class="code" href="namespace_s_p_h.html">SPH</a></div><div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;{</div><div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;    <span class="keyword">using</span> DiffusionReactionSimpleData =</div><div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;        DataDelegateSimple&lt;BodyType,</div><div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;                           DiffusionReactionParticles&lt;BaseParticlesType&gt;,</div><div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;                           DiffusionReaction&lt;BaseMaterialType&gt;&gt;;</div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div><div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;    <span class="keyword">using</span> DiffusionReactionInnerData =</div><div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;        DataDelegateInner&lt;BodyType,</div><div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;                          DiffusionReactionParticles&lt;BaseParticlesType&gt;,</div><div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;                          DiffusionReaction&lt;BaseMaterialType&gt;&gt;;</div><div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;</div><div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class </span>BodyType, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;              <span class="keyword">class </span>ContactBodyType, <span class="keyword">class </span>ContactBaseParticlesType, <span class="keyword">class </span>ContactBaseMaterialType&gt;</div><div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">using</span> DiffusionReactionContactData =</div><div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;        DataDelegateContact&lt;BodyType,</div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;                            DiffusionReactionParticles&lt;BaseParticlesType&gt;,</div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;                            DiffusionReaction&lt;BaseMaterialType&gt;,</div><div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;                            ContactBodyType, DiffusionReactionParticles&lt;ContactBaseParticlesType&gt;,</div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;                            DiffusionReaction&lt;ContactBaseMaterialType&gt;, DataDelegateEmptyBase&gt;;</div><div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;</div><div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00065"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">   65</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">DiffusionReactionInitialCondition</a></div><div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div><div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    {</div><div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">DiffusionReactionInitialCondition</a>(BodyType &amp;body);</div><div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">DiffusionReactionInitialCondition</a>(){};</div><div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;</div><div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;        <a class="code" href="class_std_large_vec_3_01_vecd_01_4.html">StdLargeVec&lt;Vecd&gt;</a> &amp;pos_;</div><div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;    };</div><div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;</div><div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">   83</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a></div><div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics.html">ParticleDynamics</a>&lt;Real&gt;,</div><div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;    {</div><div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a>(BodyType &amp;body);</div><div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html">GetDiffusionTimeStepSize</a>(){};</div><div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;</div><div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">   91</a></span>&#160;        <span class="keyword">virtual</span> Real <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">exec</a>(Real dt = 0.0)<span class="keyword"> override </span>{ <span class="keywordflow">return</span> diff_time_step_; };</div><div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;        <span class="keyword">virtual</span> Real parallel_exec(Real dt = 0.0)<span class="keyword"> override </span>{ <span class="keywordflow">return</span> <a class="code" href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">exec</a>(dt); };</div><div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;</div><div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;        Real diff_time_step_;</div><div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;    };</div><div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div><div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00103"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_inner.html">  103</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_inner.html">RelaxationOfAllDiffusionSpeciesInner</a></div><div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_interaction_dynamics_with_update.html">InteractionDynamicsWithUpdate</a>,</div><div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_inner.html">DiffusionReactionInnerData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    {</div><div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;        StdVec&lt;BaseDiffusion *&gt; species_diffusion_;</div><div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;diffusion_dt_;</div><div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        <a class="code" href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt;Real&gt;</a> &amp;Vol_;</div><div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;        <span class="keywordtype">void</span> initializeDiffusionChangeRate(<span class="keywordtype">size_t</span> particle_i);</div><div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;        <span class="keywordtype">void</span> getDiffusionChangeRate(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, Vecd &amp;e_ij, Real surface_area_ij);</div><div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> updateSpeciesDiffusion(<span class="keywordtype">size_t</span> particle_i, Real dt);</div><div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Interaction(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div><div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div><div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;</div><div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;        <span class="keyword">typedef</span> BodyType InnerBodyType;</div><div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        <span class="keyword">typedef</span> <a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a> <a class="code" href="class_s_p_h_1_1_base_particles_type.html">InnerBaseParticlesType</a>;</div><div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;        <span class="keyword">typedef</span> <a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a> <a class="code" href="class_s_p_h_1_1_base_material_type.html">InnerBaseMaterialType</a>;</div><div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;        <span class="keyword">typedef</span> <a class="code" href="class_s_p_h_1_1_base_body_relation_inner.html">BaseBodyRelationInner</a> <a class="code" href="class_s_p_h_1_1_base_body_relation_inner.html">BodyRelationType</a>;</div><div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_inner.html">RelaxationOfAllDiffusionSpeciesInner</a>(<a class="code" href="class_s_p_h_1_1_base_body_relation_inner.html">BaseBodyRelationInner</a> &amp;inner_relation);</div><div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_inner.html">RelaxationOfAllDiffusionSpeciesInner</a>(){};</div><div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;    };</div><div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;</div><div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class </span>BodyType, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a>, <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a>,</div><div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;              <span class="keyword">class </span>ContactBodyType, <span class="keyword">class </span>ContactBaseParticlesType, <span class="keyword">class </span>ContactBaseMaterialType&gt;</div><div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_complex.html">  135</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_complex.html">RelaxationOfAllDiffusionSpeciesComplex</a></div><div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_inner.html">RelaxationOfAllDiffusionSpeciesInner</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;,</div><div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_contact.html">DiffusionReactionContactData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType,</div><div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;                                              ContactBodyType, ContactBaseParticlesType, ContactBaseMaterialType&gt;</div><div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;    {</div><div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;        StdVec&lt;BaseDiffusion *&gt; species_diffusion_;</div><div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;diffusion_dt_;</div><div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt; *&gt; contact_Vol_;</div><div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;        StdVec&lt;StdVec&lt;StdLargeVec&lt;Real&gt;&gt; *&gt; contact_species_n_;</div><div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;</div><div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;        <span class="keywordtype">void</span> getDiffusionChangeRateContact(<span class="keywordtype">size_t</span> particle_i, <span class="keywordtype">size_t</span> particle_j, Vecd &amp;e_ij,</div><div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;                                           Real surface_area_ij, <span class="keyword">const</span> StdVec&lt;<a class="code" href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt;Real&gt;</a>&gt; &amp;species_n_k);</div><div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Interaction(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div><div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;</div><div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;        <span class="keyword">typedef</span> <a class="code" href="class_s_p_h_1_1_complex_body_relation.html">ComplexBodyRelation</a> <a class="code" href="class_s_p_h_1_1_base_body_relation_inner.html">BodyRelationType</a>;</div><div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_complex.html">RelaxationOfAllDiffusionSpeciesComplex</a>(<a class="code" href="class_s_p_h_1_1_complex_body_relation.html">ComplexBodyRelation</a> &amp;complex_relation);</div><div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_complex.html">RelaxationOfAllDiffusionSpeciesComplex</a>(){};</div><div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;    };</div><div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;</div><div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00162"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_initialization_r_k.html">  162</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_initialization_r_k.html">InitializationRK</a></div><div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div><div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;    {</div><div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;        StdVec&lt;BaseDiffusion *&gt; species_diffusion_;</div><div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_, &amp;species_s_;</div><div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;</div><div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;        <span class="keywordtype">void</span> initializeIntermediateValue(<span class="keywordtype">size_t</span> particle_i);</div><div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div><div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;</div><div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;        <a class="code" href="class_s_p_h_1_1_initialization_r_k.html">InitializationRK</a>(<a class="code" href="class_s_p_h_1_1_s_p_h_body.html">SPHBody</a> &amp;sph_body, StdVec&lt;<a class="code" href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt;Real&gt;</a>&gt; &amp;species_s);</div><div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_initialization_r_k.html">InitializationRK</a>(){};</div><div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;    };</div><div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;</div><div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> FirstStageType&gt;</div><div class="line"><a name="l00182"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_second_stage_r_k2.html">  182</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_second_stage_r_k2.html">SecondStageRK2</a> : <span class="keyword">public</span> FirstStageType</div><div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;    {</div><div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;        StdVec&lt;BaseDiffusion *&gt; species_diffusion_;</div><div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;diffusion_dt_;</div><div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;</div><div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_s_;</div><div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> updateSpeciesDiffusion(<span class="keywordtype">size_t</span> particle_i, Real dt) <span class="keyword">override</span>;</div><div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;</div><div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;        <a class="code" href="class_s_p_h_1_1_second_stage_r_k2.html">SecondStageRK2</a>(<span class="keyword">typename</span> FirstStageType::BodyRelationType &amp;body_relation,</div><div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;                       StdVec&lt;<a class="code" href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt;Real&gt;</a>&gt; &amp;species_s);</div><div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_second_stage_r_k2.html">SecondStageRK2</a>(){};</div><div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;    };</div><div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;</div><div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> FirstStageType&gt;</div><div class="line"><a name="l00204"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">  204</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">RelaxationOfAllDiffusionSpeciesRK2</a> : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics.html">ParticleDynamics</a>&lt;void&gt;</div><div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;    {</div><div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;        StdVec&lt;BaseDiffusion *&gt; species_diffusion_;</div><div class="line"><a name="l00209"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#a7ed2d6d54334c9fd0b375063bbfaadcf">  209</a></span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#a7ed2d6d54334c9fd0b375063bbfaadcf">species_s_</a>;</div><div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;</div><div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;        <a class="code" href="class_s_p_h_1_1_initialization_r_k.html">InitializationRK</a>&lt;<span class="keyword">typename</span> FirstStageType::InnerBodyType,</div><div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;                         <span class="keyword">typename</span> FirstStageType::InnerBaseParticlesType,</div><div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;                         <span class="keyword">typename</span> FirstStageType::InnerBaseMaterialType&gt;</div><div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;            rk2_initialization_;</div><div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;        <a class="code" href="class_s_p_h_1_1_first_stage_type.html">FirstStageType</a> rk2_1st_stage_;</div><div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;        <a class="code" href="class_s_p_h_1_1_second_stage_r_k2.html">SecondStageRK2&lt;FirstStageType&gt;</a> rk2_2nd_stage_;</div><div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;</div><div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">RelaxationOfAllDiffusionSpeciesRK2</a>(<span class="keyword">typename</span> FirstStageType::BodyRelationType &amp;body_relation);</div><div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">RelaxationOfAllDiffusionSpeciesRK2</a>(){};</div><div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;</div><div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#ad1f02306798f50c9cbce664ea7c02105">exec</a>(Real dt = 0.0) <span class="keyword">override</span>;</div><div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> parallel_exec(Real dt = 0.0) <span class="keyword">override</span>;</div><div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;    };</div><div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;</div><div class="line"><a name="l00226"></a><span class="lineno"><a class="line" href="struct_s_p_h_1_1_update_a_reaction_species.html">  226</a></span>&#160;    <span class="keyword">struct </span><a class="code" href="struct_s_p_h_1_1_update_a_reaction_species.html">UpdateAReactionSpecies</a></div><div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;    {</div><div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;        Real operator()(Real input, Real production_rate, Real loss_rate, Real dt)<span class="keyword"> const</span></div><div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;            <span class="keywordflow">return</span> input * exp(-loss_rate * dt) + production_rate * (1.0 - exp(-loss_rate * dt)) / (loss_rate + TinyReal);</div><div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;        };</div><div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;    };</div><div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;</div><div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00239"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">  239</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">RelaxationOfAllReactionsForward</a></div><div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div><div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;    {</div><div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a> *species_reaction_;</div><div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;        <a class="code" href="struct_s_p_h_1_1_update_a_reaction_species.html">UpdateAReactionSpecies</a> updateAReactionSpecies;</div><div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;</div><div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div><div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;</div><div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">RelaxationOfAllReactionsForward</a>(BodyType &amp;body);</div><div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">RelaxationOfAllReactionsForward</a>(){};</div><div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;    };</div><div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;</div><div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00260"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">  260</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">RelaxationOfAllReactionsBackward</a></div><div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div><div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;    {</div><div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;        <a class="code" href="class_s_p_h_1_1_base_reaction_model.html">BaseReactionModel</a> *species_reaction_;</div><div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;        <a class="code" href="struct_s_p_h_1_1_update_a_reaction_species.html">UpdateAReactionSpecies</a> updateAReactionSpecies;</div><div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;</div><div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;        <span class="keyword">virtual</span> <span class="keywordtype">void</span> Update(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0) <span class="keyword">override</span>;</div><div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;</div><div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">RelaxationOfAllReactionsBackward</a>(BodyType &amp;body);</div><div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">RelaxationOfAllReactionsBackward</a>(){};</div><div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;    };</div><div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;</div><div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BodyPartByParticleType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00281"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_constrain_diffusion_body_region.html">  281</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_constrain_diffusion_body_region.html">ConstrainDiffusionBodyRegion</a></div><div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_part_simple_dynamics_by_particle.html">PartSimpleDynamicsByParticle</a>,</div><div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;    {</div><div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;        <a class="code" href="class_s_p_h_1_1_constrain_diffusion_body_region.html">ConstrainDiffusionBodyRegion</a>(BodyType &amp;body, BodyPartByParticleType &amp;body_part)</div><div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;            : <a class="code" href="class_s_p_h_1_1_part_simple_dynamics_by_particle.html">PartSimpleDynamicsByParticle</a>(body, body_part),</div><div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;              <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a>(body),</div><div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;              pos_(this-&gt;particles_-&gt;pos_), species_n_(this-&gt;particles_-&gt;species_n_){};</div><div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_constrain_diffusion_body_region.html">ConstrainDiffusionBodyRegion</a>(){};</div><div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;</div><div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;        <a class="code" href="class_std_large_vec_3_01_vecd_01_4.html">StdLargeVec&lt;Vecd&gt;</a> &amp;pos_;</div><div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;    };</div><div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;</div><div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00303"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_diffusion_based_mapping.html">  303</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a></div><div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>,</div><div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;    {</div><div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a>(BodyType &amp;body)</div><div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;            : <a class="code" href="class_s_p_h_1_1_particle_dynamics_simple.html">ParticleDynamicsSimple</a>(body),</div><div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;              <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a>(body),</div><div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;              pos_(this-&gt;particles_-&gt;pos_), species_n_(this-&gt;particles_-&gt;species_n_){};</div><div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_diffusion_based_mapping.html">DiffusionBasedMapping</a>(){};</div><div class="line"><a name="l00313"></a><span class="lineno">  313</span>&#160;</div><div class="line"><a name="l00314"></a><span class="lineno">  314</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00315"></a><span class="lineno">  315</span>&#160;        <a class="code" href="class_std_large_vec_3_01_vecd_01_4.html">StdLargeVec&lt;Vecd&gt;</a> &amp;pos_;</div><div class="line"><a name="l00316"></a><span class="lineno">  316</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00317"></a><span class="lineno">  317</span>&#160;    };</div><div class="line"><a name="l00318"></a><span class="lineno">  318</span>&#160;</div><div class="line"><a name="l00323"></a><span class="lineno">  323</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00324"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_total_averaged_parameter_on_diffusion_body.html">  324</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_total_averaged_parameter_on_diffusion_body.html">TotalAveragedParameterOnDiffusionBody</a></div><div class="line"><a name="l00325"></a><span class="lineno">  325</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_particle_dynamics_reduce.html">ParticleDynamicsReduce</a>&lt;Real, ReduceSum&lt;Real&gt;&gt;,</div><div class="line"><a name="l00326"></a><span class="lineno">  326</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00327"></a><span class="lineno">  327</span>&#160;    {</div><div class="line"><a name="l00328"></a><span class="lineno">  328</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00329"></a><span class="lineno">  329</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_total_averaged_parameter_on_diffusion_body.html">TotalAveragedParameterOnDiffusionBody</a>(BodyType &amp;body, <span class="keyword">const</span> std::string &amp;species_name)</div><div class="line"><a name="l00330"></a><span class="lineno">  330</span>&#160;            : <a class="code" href="class_s_p_h_1_1_particle_dynamics_reduce.html">ParticleDynamicsReduce&lt;Real, ReduceSum&lt;Real&gt;</a>&gt;(body),</div><div class="line"><a name="l00331"></a><span class="lineno">  331</span>&#160;              <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a>(body),</div><div class="line"><a name="l00332"></a><span class="lineno">  332</span>&#160;              species_n_(this-&gt;particles_-&gt;species_n_), species_name_(species_name)</div><div class="line"><a name="l00333"></a><span class="lineno">  333</span>&#160;        {</div><div class="line"><a name="l00334"></a><span class="lineno">  334</span>&#160;            quantity_name_ = <span class="stringliteral">&quot;TotalAveragedParameterOnDiffusionBody&quot;</span>;</div><div class="line"><a name="l00335"></a><span class="lineno">  335</span>&#160;            <a class="code" href="class_s_p_h_1_1_particle_dynamics_reduce.html#a0da29bb747776e41caa375d67be5b656">initial_reference_</a> = Real(0);</div><div class="line"><a name="l00336"></a><span class="lineno">  336</span>&#160;            phi_ = this-&gt;material_-&gt;SpeciesIndexMap()[species_name_];</div><div class="line"><a name="l00337"></a><span class="lineno">  337</span>&#160;        }</div><div class="line"><a name="l00338"></a><span class="lineno">  338</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_total_averaged_parameter_on_diffusion_body.html">TotalAveragedParameterOnDiffusionBody</a>(){};</div><div class="line"><a name="l00339"></a><span class="lineno">  339</span>&#160;</div><div class="line"><a name="l00340"></a><span class="lineno">  340</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00341"></a><span class="lineno">  341</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00342"></a><span class="lineno">  342</span>&#160;        std::string species_name_;</div><div class="line"><a name="l00343"></a><span class="lineno">  343</span>&#160;        <span class="keywordtype">size_t</span> phi_;</div><div class="line"><a name="l00344"></a><span class="lineno">  344</span>&#160;        Real ReduceFunction(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0)<span class="keyword"> override</span></div><div class="line"><a name="l00345"></a><span class="lineno">  345</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00346"></a><span class="lineno">  346</span>&#160;            <span class="keywordflow">return</span> species_n_[phi_][index_i] / this-&gt;base_particles_-&gt;total_real_particles_;</div><div class="line"><a name="l00347"></a><span class="lineno">  347</span>&#160;        }</div><div class="line"><a name="l00348"></a><span class="lineno">  348</span>&#160;    };</div><div class="line"><a name="l00349"></a><span class="lineno">  349</span>&#160;</div><div class="line"><a name="l00354"></a><span class="lineno">  354</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">class</span> BodyType, <span class="keyword">class</span> BaseParticlesType, <span class="keyword">class</span> BaseMaterialType&gt;</div><div class="line"><a name="l00355"></a><span class="lineno"><a class="line" href="class_s_p_h_1_1_total_averaged_parameter_on_partly_diffusion_body.html">  355</a></span>&#160;    <span class="keyword">class </span><a class="code" href="class_s_p_h_1_1_total_averaged_parameter_on_partly_diffusion_body.html">TotalAveragedParameterOnPartlyDiffusionBody</a></div><div class="line"><a name="l00356"></a><span class="lineno">  356</span>&#160;        : <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_part_dynamics_by_particle_reduce.html">PartDynamicsByParticleReduce</a>&lt;Real, ReduceSum&lt;Real&gt;&gt;,</div><div class="line"><a name="l00357"></a><span class="lineno">  357</span>&#160;          <span class="keyword">public</span> <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData</a>&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</div><div class="line"><a name="l00358"></a><span class="lineno">  358</span>&#160;    {</div><div class="line"><a name="l00359"></a><span class="lineno">  359</span>&#160;    <span class="keyword">public</span>:</div><div class="line"><a name="l00360"></a><span class="lineno">  360</span>&#160;        <span class="keyword">explicit</span> <a class="code" href="class_s_p_h_1_1_total_averaged_parameter_on_partly_diffusion_body.html">TotalAveragedParameterOnPartlyDiffusionBody</a>(BodyType &amp;body,</div><div class="line"><a name="l00361"></a><span class="lineno">  361</span>&#160;                                                             <a class="code" href="class_s_p_h_1_1_body_part_by_particle.html">BodyPartByParticle</a> &amp;body_part, <span class="keyword">const</span> std::string &amp;species_name)</div><div class="line"><a name="l00362"></a><span class="lineno">  362</span>&#160;            : <a class="code" href="class_s_p_h_1_1_part_dynamics_by_particle_reduce.html">PartDynamicsByParticleReduce&lt;Real, ReduceSum&lt;Real&gt;</a>&gt;(body, body_part),</div><div class="line"><a name="l00363"></a><span class="lineno">  363</span>&#160;              <a class="code" href="class_s_p_h_1_1_data_delegate_simple.html">DiffusionReactionSimpleData&lt;BodyType, BaseParticlesType, BaseMaterialType&gt;</a>(body),</div><div class="line"><a name="l00364"></a><span class="lineno">  364</span>&#160;              species_n_(this-&gt;particles_-&gt;species_n_), species_name_(species_name)</div><div class="line"><a name="l00365"></a><span class="lineno">  365</span>&#160;        {</div><div class="line"><a name="l00366"></a><span class="lineno">  366</span>&#160;            quantity_name_ = <span class="stringliteral">&quot;TotalAveragedParameterOnPartlyDiffusionBody&quot;</span>;</div><div class="line"><a name="l00367"></a><span class="lineno">  367</span>&#160;            initial_reference_ = Real(0);</div><div class="line"><a name="l00368"></a><span class="lineno">  368</span>&#160;            phi_ = this-&gt;material_-&gt;SpeciesIndexMap()[species_name_];</div><div class="line"><a name="l00369"></a><span class="lineno">  369</span>&#160;        };</div><div class="line"><a name="l00370"></a><span class="lineno">  370</span>&#160;        <span class="keyword">virtual</span> ~<a class="code" href="class_s_p_h_1_1_total_averaged_parameter_on_partly_diffusion_body.html">TotalAveragedParameterOnPartlyDiffusionBody</a>(){};</div><div class="line"><a name="l00371"></a><span class="lineno">  371</span>&#160;</div><div class="line"><a name="l00372"></a><span class="lineno">  372</span>&#160;    <span class="keyword">protected</span>:</div><div class="line"><a name="l00373"></a><span class="lineno">  373</span>&#160;        StdVec&lt;StdLargeVec&lt;Real&gt;&gt; &amp;species_n_;</div><div class="line"><a name="l00374"></a><span class="lineno">  374</span>&#160;        std::string species_name_;</div><div class="line"><a name="l00375"></a><span class="lineno">  375</span>&#160;        <span class="keywordtype">size_t</span> phi_;</div><div class="line"><a name="l00376"></a><span class="lineno">  376</span>&#160;        Real ReduceFunction(<span class="keywordtype">size_t</span> index_i, Real dt = 0.0)<span class="keyword"> override</span></div><div class="line"><a name="l00377"></a><span class="lineno">  377</span>&#160;<span class="keyword">        </span>{</div><div class="line"><a name="l00378"></a><span class="lineno">  378</span>&#160;            <span class="keywordflow">return</span> species_n_[phi_][index_i] / body_part_particles_.size();</div><div class="line"><a name="l00379"></a><span class="lineno">  379</span>&#160;        }</div><div class="line"><a name="l00380"></a><span class="lineno">  380</span>&#160;    };</div><div class="line"><a name="l00381"></a><span class="lineno">  381</span>&#160;}</div><div class="line"><a name="l00382"></a><span class="lineno">  382</span>&#160;<span class="preprocessor">#endif // PARTICLE_DYNAMICS_DIFFUSION_REACTION_H</span></div><div class="ttc" id="class_std_large_vec_3_01_real_01_4_html"><div class="ttname"><a href="class_std_large_vec_3_01_real_01_4.html">StdLargeVec&lt; Real &gt;</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_data_delegate_inner_html"><div class="ttname"><a href="class_s_p_h_1_1_data_delegate_inner.html">SPH::DataDelegateInner</a></div><div class="ttdoc">prepare data for inner particle dynamics </div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:216</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html_a7ed2d6d54334c9fd0b375063bbfaadcf"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#a7ed2d6d54334c9fd0b375063bbfaadcf">SPH::RelaxationOfAllDiffusionSpeciesRK2::species_s_</a></div><div class="ttdeci">StdVec&lt; StdLargeVec&lt; Real &gt; &gt; species_s_</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:209</div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_simple_html"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics_simple.html">SPH::ParticleDynamicsSimple</a></div><div class="ttdoc">Simple particle dynamics without considering particle interaction. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_algorithms.h:48</div></div>
<div class="ttc" id="class_s_p_h_1_1_body_part_by_particle_html"><div class="ttname"><a href="class_s_p_h_1_1_body_part_by_particle.html">SPH::BodyPartByParticle</a></div><div class="ttdoc">A body part with a collection of particles. </div><div class="ttdef"><b>Definition:</b> base_body_part.h:64</div></div>
<div class="ttc" id="diffusion__reaction__particles_8h_html"><div class="ttname"><a href="diffusion__reaction__particles_8h.html">diffusion_reaction_particles.h</a></div><div class="ttdoc">This is the derived class of diffusion reaction particles. </div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html">SPH::RelaxationOfAllDiffusionSpeciesRK2</a></div><div class="ttdoc">Compute the diffusion relaxation process of all species with second order Runge-Kutta time stepping...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:204</div></div>
<div class="ttc" id="class_s_p_h_1_1_first_stage_type_html"><div class="ttname"><a href="class_s_p_h_1_1_first_stage_type.html">FirstStageType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_part_simple_dynamics_by_particle_html"><div class="ttname"><a href="class_s_p_h_1_1_part_simple_dynamics_by_particle.html">SPH::PartSimpleDynamicsByParticle</a></div><div class="ttdoc">Abstract class for body part simple particle dynamics. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_bodypart.h:70</div></div>
<div class="ttc" id="class_s_p_h_1_1_total_averaged_parameter_on_partly_diffusion_body_html"><div class="ttname"><a href="class_s_p_h_1_1_total_averaged_parameter_on_partly_diffusion_body.html">SPH::TotalAveragedParameterOnPartlyDiffusionBody</a></div><div class="ttdoc">Computing the total averaged parameter on partly diffusion body. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:355</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_inner_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_inner.html">SPH::RelaxationOfAllDiffusionSpeciesInner</a></div><div class="ttdoc">Compute the diffusion relaxation process of all species. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:103</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_reactions_forward_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_forward.html">SPH::RelaxationOfAllReactionsForward</a></div><div class="ttdoc">Compute the reaction process of all species by forward splitting. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:239</div></div>
<div class="ttc" id="class_std_large_vec_3_01_vecd_01_4_html"><div class="ttname"><a href="class_std_large_vec_3_01_vecd_01_4.html">StdLargeVec&lt; Vecd &gt;</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_reduce_html"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics_reduce.html">SPH::ParticleDynamicsReduce</a></div><div class="ttdoc">Base abstract class for reduce. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_algorithms.h:69</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_particles_type_html"><div class="ttname"><a href="class_s_p_h_1_1_base_particles_type.html">BaseParticlesType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_based_mapping_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_based_mapping.html">SPH::DiffusionBasedMapping</a></div><div class="ttdoc">Mapping inside of body according to diffusion. This is a abstract class to be override for case speci...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:303</div></div>
<div class="ttc" id="class_s_p_h_1_1_get_diffusion_time_step_size_html"><div class="ttname"><a href="class_s_p_h_1_1_get_diffusion_time_step_size.html">SPH::GetDiffusionTimeStepSize</a></div><div class="ttdoc">Computing the time step size based on diffusion coefficient and particle smoothing length...</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:83</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_complex_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_complex.html">SPH::RelaxationOfAllDiffusionSpeciesComplex</a></div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:135</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2_html_ad1f02306798f50c9cbce664ea7c02105"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_diffusion_species_r_k2.html#ad1f02306798f50c9cbce664ea7c02105">SPH::RelaxationOfAllDiffusionSpeciesRK2::exec</a></div><div class="ttdeci">virtual void exec(Real dt=0.0) override</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.hpp:241</div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_reduce_html_a0da29bb747776e41caa375d67be5b656"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics_reduce.html#a0da29bb747776e41caa375d67be5b656">SPH::ParticleDynamicsReduce&lt; Real, ReduceSum&lt; Real &gt; &gt;::initial_reference_</a></div><div class="ttdeci">Real initial_reference_</div><div class="ttdef"><b>Definition:</b> particle_dynamics_algorithms.h:104</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_reaction_model_html"><div class="ttname"><a href="class_s_p_h_1_1_base_reaction_model.html">SPH::BaseReactionModel</a></div><div class="ttdoc">Base class for all reaction models. </div><div class="ttdef"><b>Definition:</b> diffusion_reaction.h:163</div></div>
<div class="ttc" id="class_s_p_h_1_1_data_delegate_contact_html"><div class="ttname"><a href="class_s_p_h_1_1_data_delegate_contact.html">SPH::DataDelegateContact</a></div><div class="ttdoc">prepare data for contact particle dynamics </div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:240</div></div>
<div class="ttc" id="class_s_p_h_1_1_get_diffusion_time_step_size_html_abbafdb225bf35578cb3d8d891f54b1e9"><div class="ttname"><a href="class_s_p_h_1_1_get_diffusion_time_step_size.html#abbafdb225bf35578cb3d8d891f54b1e9">SPH::GetDiffusionTimeStepSize::exec</a></div><div class="ttdeci">virtual Real exec(Real dt=0.0) override</div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:91</div></div>
<div class="ttc" id="class_s_p_h_1_1_diffusion_reaction_initial_condition_html"><div class="ttname"><a href="class_s_p_h_1_1_diffusion_reaction_initial_condition.html">SPH::DiffusionReactionInitialCondition</a></div><div class="ttdoc">pure abstract class for initial conditions </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:65</div></div>
<div class="ttc" id="class_s_p_h_1_1_second_stage_r_k2_html"><div class="ttname"><a href="class_s_p_h_1_1_second_stage_r_k2.html">SPH::SecondStageRK2</a></div><div class="ttdoc">the second stage of the 2nd-order Runge-Kutta scheme </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:182</div></div>
<div class="ttc" id="class_s_p_h_1_1_relaxation_of_all_reactions_backward_html"><div class="ttname"><a href="class_s_p_h_1_1_relaxation_of_all_reactions_backward.html">SPH::RelaxationOfAllReactionsBackward</a></div><div class="ttdoc">Compute the reaction process of all species by backward splitting. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:260</div></div>
<div class="ttc" id="class_s_p_h_1_1_complex_body_relation_html"><div class="ttname"><a href="class_s_p_h_1_1_complex_body_relation.html">SPH::ComplexBodyRelation</a></div><div class="ttdoc">The relation combined an inner and a contact body relation. The interaction is in a inner-boundary-co...</div><div class="ttdef"><b>Definition:</b> complex_body_relation.h:42</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_material_type_html"><div class="ttname"><a href="class_s_p_h_1_1_base_material_type.html">BaseMaterialType</a></div></div>
<div class="ttc" id="class_s_p_h_1_1_s_p_h_body_html"><div class="ttname"><a href="class_s_p_h_1_1_s_p_h_body.html">SPH::SPHBody</a></div><div class="ttdoc">SPHBody is a base body with basic data and functions. Its derived class can be a real fluid body...</div><div class="ttdef"><b>Definition:</b> base_body.h:61</div></div>
<div class="ttc" id="class_s_p_h_1_1_part_dynamics_by_particle_reduce_html"><div class="ttname"><a href="class_s_p_h_1_1_part_dynamics_by_particle_reduce.html">SPH::PartDynamicsByParticleReduce</a></div><div class="ttdoc">reduce operation in a Lagrangian contrained region. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_bodypart.h:227</div></div>
<div class="ttc" id="class_s_p_h_1_1_interaction_dynamics_with_update_html"><div class="ttname"><a href="class_s_p_h_1_1_interaction_dynamics_with_update.html">SPH::InteractionDynamicsWithUpdate</a></div><div class="ttdoc">This class includes an interaction and a update steps. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_algorithms.h:160</div></div>
<div class="ttc" id="class_s_p_h_1_1_base_body_relation_inner_html"><div class="ttname"><a href="class_s_p_h_1_1_base_body_relation_inner.html">SPH::BaseBodyRelationInner</a></div><div class="ttdoc">The abstract relation within a SPH body. </div><div class="ttdef"><b>Definition:</b> base_body_relation.h:117</div></div>
<div class="ttc" id="class_s_p_h_1_1_data_delegate_simple_html"><div class="ttname"><a href="class_s_p_h_1_1_data_delegate_simple.html">SPH::DataDelegateSimple</a></div><div class="ttdoc">prepare data for simple particle dynamics. </div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:185</div></div>
<div class="ttc" id="class_s_p_h_1_1_constrain_diffusion_body_region_html"><div class="ttname"><a href="class_s_p_h_1_1_constrain_diffusion_body_region.html">SPH::ConstrainDiffusionBodyRegion</a></div><div class="ttdoc">set boundary condition for diffusion problem </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:281</div></div>
<div class="ttc" id="class_s_p_h_1_1_initialization_r_k_html"><div class="ttname"><a href="class_s_p_h_1_1_initialization_r_k.html">SPH::InitializationRK</a></div><div class="ttdoc">initialization of a runge-kutta integration scheme </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:162</div></div>
<div class="ttc" id="struct_s_p_h_1_1_update_a_reaction_species_html"><div class="ttname"><a href="struct_s_p_h_1_1_update_a_reaction_species.html">SPH::UpdateAReactionSpecies</a></div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:226</div></div>
<div class="ttc" id="class_s_p_h_1_1_total_averaged_parameter_on_diffusion_body_html"><div class="ttname"><a href="class_s_p_h_1_1_total_averaged_parameter_on_diffusion_body.html">SPH::TotalAveragedParameterOnDiffusionBody</a></div><div class="ttdoc">Computing the total averaged parameter on the whole diffusion body. </div><div class="ttdef"><b>Definition:</b> particle_dynamics_diffusion_reaction.h:324</div></div>
<div class="ttc" id="namespace_s_p_h_html"><div class="ttname"><a href="namespace_s_p_h.html">SPH</a></div><div class="ttdef"><b>Definition:</b> solid_body_supplementary.cpp:9</div></div>
<div class="ttc" id="class_s_p_h_1_1_particle_dynamics_html"><div class="ttname"><a href="class_s_p_h_1_1_particle_dynamics.html">SPH::ParticleDynamics</a></div><div class="ttdoc">The base class for all particle dynamics This class contains the only two interface functions availab...</div><div class="ttdef"><b>Definition:</b> base_particle_dynamics.h:145</div></div>
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